In [17]:
from livelossplot import PlotLossesKeras
import os
import pandas as pd
from sklearn.model_selection import train_test_split
import numpy as np
from sklearn.model_selection import GroupShuffleSplit
from IPython.display import display # Allows the use of display() for DataFrames
import matplotlib.pyplot as plt
#import seaborn as sns
import cv2
import random
import shutil
import pathlib
%matplotlib inline
np.random.seed(100)
Prepare data¶
In [18]:
df = pd.read_csv("train.csv", header = 0)
display(df.std())
total_images = len(df)
# drop rows with new_whale because it is used to label various unknown flukes yet
#df = df[df.Id != 'new_whale']
# use targets with 3+ samples
df = df.groupby("Id").filter(lambda x: len(x) >= 3)
# Use top N targets by image count
value_counts = df.Id.value_counts()
top_hitters = value_counts.nlargest(10).index
df = df[df['Id'].isin(top_hitters)]
fig, ax = plt.subplots()
ax.set_yscale('log')
ax.set_ylabel("Whales")
ax.set_xlabel("Images per whale")
value_counts.hist(ax=ax,figsize=(20,5),bins=10, bottom=1)
classes = df.Id.unique()
num_classes = len(classes)
X_train = []; y_train = []
X_test = []; y_test = []
X_valid = []; y_valid = []
for whale_id in classes:
df_whale = df[df.Id == whale_id]
X_whale = np.array([os.path.join(os.getcwd(), 'train', s) for s in df_whale.Image])
y_whale = np.array(df_whale.Id.values)
X_train_whale, X_test_whale, y_train_whale, y_test_whale = \
train_test_split(X_whale, y_whale, test_size=0.2, random_state=1)
X_test.extend(X_test_whale)
y_test.extend(y_test_whale)
X_train_whale, X_valid_whale, y_train_whale, y_valid_whale = \
train_test_split(X_train_whale, y_train_whale, test_size=0.2, random_state=1)
X_train.extend(X_train_whale)
y_train.extend(y_train_whale)
X_valid.extend(X_valid_whale)
y_valid.extend(y_valid_whale)
print('\nThere are %d total images.' % total_images)
print("Trainable...")
print('There are %d total classes.' % num_classes)
print('There are %d training images.' % len(X_train))
print('There are %d validation images.' % len(X_valid))
print('There are %d test images.' % len(X_test))
print("After data filtering")
df.describe()
print(classes)
workers = 8
batch_size = 32
Visualize 12 random training images¶
In [19]:
def visualize_img(img_path, ax):
img = cv2.imread(img_path)
ax.imshow(cv2.cvtColor(img, cv2.COLOR_BGR2RGB))
fig = plt.figure(figsize=(50, 30))
num_images = 12
rand_images = random.sample(X_train, num_images)
for i, file in enumerate(rand_images):
ax = fig.add_subplot(3, 4, i + 1, xticks=[], yticks=[])
visualize_img(file, ax)
Visualize random whale from top hitters¶
In [20]:
random_whale = random.sample(list(top_hitters),1)
print(random_whale)
whale_images = list(df[df['Id'].isin(random_whale)]['Image'])
files = [s for s in X_train if any(w in s for w in whale_images)]
fig = plt.figure(figsize=(50, 30))
for i, file in enumerate(files[:12]):
ax = fig.add_subplot(3, 4, i + 1, xticks=[], yticks=[])
visualize_img(file, ax)
Prepare Dataset for ImageDataGenerator¶
In [21]:
def copy_class_of_files(files, dst, labels):
for idx, val in enumerate(files):
dst_dir = os.path.join(dst, labels[idx])
pathlib.Path(dst_dir).mkdir(parents=True, exist_ok=True)
shutil.copy(val, dst_dir)
shutil.rmtree('./data', ignore_errors=True)
copy_class_of_files(X_train, 'data/train', y_train)
copy_class_of_files(X_valid, 'data/valid', y_valid)
copy_class_of_files(X_test, 'data/test', y_test)
Load CNN without top layer¶
In [22]:
#from keras.applications.inception_resnet_v2 import InceptionResNetV2
from keras.applications.vgg16 import VGG16
from keras.applications.vgg19 import VGG19
from keras.models import Model
#define VGG19 model
image_side_size = 150
image_dim = (image_side_size, image_side_size, 3)
base_model = VGG19(weights='imagenet', include_top=False,
input_tensor=None, input_shape=image_dim,
pooling=None)
cut_off_layer = base_model.get_layer('block4_pool')
# define InceptionResNetV2 model
# image_side_size = 299
# image_dim = (image_side_size, image_side_size, 3)
# base_model = InceptionResNetV2(weights='imagenet', include_top=False,
# input_tensor=None, input_shape=image_dim,
# pooling=None)
# cut_off_layer = base_model.get_layer('mixed_7a')
print(f"Layers {len(base_model.layers)}")
# freeze weights in all layers of the base model
for layer in base_model.layers:
layer.trainable = False
print("Complete model before trimming")
base_model.summary()
# https://github.com/keras-team/keras/issues/8909#issuecomment-354406145
# https://github.com/keras-team/keras/issues/2371
base_model = Model(base_model.input, cut_off_layer.output)
print(f'Last base layer: {base_model.output}')
print("Trimmed model")
base_model.summary()
Top layer specific to our problem¶
In [23]:
from keras.models import Sequential, Model
from keras.layers import Dropout, Flatten, Dense, GlobalAveragePooling2D
# add a global spatial average pooling layer
x = base_model.output
x = GlobalAveragePooling2D()(x)
x = Dense(512, activation="relu")(x)
x = Dropout(0.2)(x)
x = Dense(512, activation="relu")(x)
x = Dropout(0.2)(x)
predictions = Dense(num_classes, activation='softmax')(x)
# this is the model we will train
model = Model(inputs=base_model.input, outputs=predictions)
Compile model¶
In [24]:
from keras.optimizers import RMSprop
model.compile(loss='categorical_crossentropy',
optimizer=RMSprop(lr=0.0001),
metrics=['accuracy'])
Define image generators¶
In [25]:
from keras.preprocessing.image import ImageDataGenerator
target_size = (image_side_size, image_side_size)
train_datagen = ImageDataGenerator(
rescale=1./255,
horizontal_flip=True,
vertical_flip=True,
rotation_range=40,
width_shift_range=0.2,
height_shift_range=0.2,
zoom_range=0.2,
shear_range=0.2,
fill_mode='nearest')
valid_datagen = ImageDataGenerator(rescale=1./255)
print("Train generator")
train_generator = train_datagen.flow_from_directory(
'data/train',
target_size = target_size,
class_mode = 'categorical',
batch_size = batch_size,
shuffle=True)
print("Valid generator")
valid_generator = valid_datagen.flow_from_directory(
'data/valid',
target_size = target_size,
class_mode = 'categorical',
batch_size = batch_size)
In [26]:
from keras.callbacks import ModelCheckpoint, EarlyStopping, TensorBoard, ReduceLROnPlateau
from time import time
best_weights_path=f'whale.flukes.{num_classes}_classes.weights.best.hdf5'
# train the model
checkpointer = ModelCheckpoint(filepath=best_weights_path, verbose=1, save_best_only=True)
# Stop the training if the model shows no improvement
stopper = EarlyStopping(monitor='val_loss',
min_delta=0.005,
patience=100,
verbose=1,
mode='auto')
# Reduce learning rate when a metric has stopped improving.
reduce_lr = ReduceLROnPlateau(monitor='val_loss',
factor=0.7,
patience=20,
min_lr=0.0000001,
verbose=1)
tensorboard = TensorBoard(log_dir="./logs/final/{}".format(time()),
batch_size=batch_size,
write_graph=True,
write_images=True,
histogram_freq=0,
write_grads=True)
model.fit_generator(generator=train_generator,
epochs=1000,
steps_per_epoch = len(X_train)//batch_size,
validation_data=valid_generator,
validation_steps = len(X_valid)//batch_size,
callbacks=[checkpointer, stopper, reduce_lr,
PlotLossesKeras(),
tensorboard],
verbose=1, workers=workers)
Out[26]:
Load the Model with the Best Validation Loss¶
In [27]:
model.load_weights(best_weights_path)
Calculate Classification Accuracy on Test Set¶
In [28]:
test_datagen = ImageDataGenerator(rescale=1. / 255)
test_generator = test_datagen.flow_from_directory(
"data/test",
target_size=target_size,
batch_size=batch_size,
class_mode='categorical', shuffle=False)
score = model.evaluate_generator(
generator=test_generator,
workers=workers)
print("Loss: ", score[0], "Accuracy: ", score[1])
scores = model.predict_generator(
generator=test_generator,
workers=workers)
Print confusion matrix¶
In [29]:
from sklearn.metrics import confusion_matrix
import itertools
def plot_confusion_matrix(cm, classes,
normalize=False,
title='Confusion matrix',
cmap=plt.cm.Blues):
"""
This function prints and plots the confusion matrix.
Normalization can be applied by setting `normalize=True`.
"""
if normalize:
cm = cm.astype('float') / cm.sum(axis=1)[:, np.newaxis]
print("Normalized confusion matrix")
else:
print('Confusion matrix, without normalization')
plt.imshow(cm, interpolation='nearest', cmap=cmap)
plt.title(title)
plt.colorbar()
tick_marks = np.arange(len(classes))
plt.xticks(tick_marks, classes, rotation=45)
plt.yticks(tick_marks, classes)
fmt = '.2f' if normalize else 'd'
thresh = cm.max() / 2.
for i, j in itertools.product(range(cm.shape[0]), range(cm.shape[1])):
plt.text(j, i, format(cm[i, j], fmt),
horizontalalignment="center",
color="white" if cm[i, j] > thresh else "black")
plt.tight_layout()
plt.ylabel('True label')
plt.xlabel('Predicted label')
cnf_matrix = confusion_matrix(test_generator.classes, list(map(lambda x: np.argmax(x), scores)))
np.set_printoptions(precision=2)
# Plot non-normalized confusion matrix
plt.figure(figsize=(80,20))
plot_confusion_matrix(cnf_matrix, classes=classes, title='Confusion matrix, without normalization')
# Plot normalized confusion matrix
plt.figure(figsize=(80,20))
plot_confusion_matrix(cnf_matrix, classes=classes, normalize=True, title='Normalized confusion matrix')
plt.show()
Write classification result¶
In [30]:
import csv
import ntpath
with open('predictions.csv', 'w') as csvfile:
fieldnames = ['Image', 'Id']
writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
writer.writeheader()
for idx, file_name in enumerate(X_test):
probs = scores[idx]
_, sorted_classes = zip(*sorted(zip(probs, classes), reverse=True))
writer.writerow(dict(zip(fieldnames, [ntpath.basename(file_name), ' '.join(sorted_classes[:3])])))